Genomics Efforts (genomics + effort)

Distribution by Scientific Domains

Kinds of Genomics Efforts

  • structural genomics effort

  • Selected Abstracts

    The ybeY protein from Escherichia coli is a metalloprotein

    Chenyang Zhan
    The three-dimensional crystallographic structure of the ybeY protein from Escherichia coli (SwissProt entry P77385) is reported at 2.7, resolution. YbeY is a hypothetical protein that belongs to the UPF0054 family. The structure reveals that the protein binds a metal ion in a tetrahedral geometry. Three coordination sites are provided by histidine residues, while the fourth might be a water molecule that is not seen in the diffraction map because of its relatively low resolution. X-ray fluorescence analysis of the purified protein suggests that the metal is a nickel ion. The structure of ybeY and its sequence similarity to a number of predicted metal-dependent hydrolases provides a functional assignment for this protein family. The figures and tables of this paper were prepared using semi-automated tools, termed the Autopublish server, developed by the New York Structural GenomiX Research Consortium, with the goal of facilitating the rapid publication of crystallographic structures that emanate from worldwide Structural Genomics efforts, including the NIH-funded Protein Structure Initiative. [source]

    Synchrotron techniques for metalloproteins and human disease in post genome era

    S. Samar Hasnain
    Metalloproteins make up some 30% of proteins in known genomes. Metalloproteins are a special class of proteins that utilise the unique properties of metal atoms in conjunction with the macromolecular assembly to perform life-sustaining processes. A number of metalloproteins are known to be involved in many disease states including ageing processes. The incorporation of the metal ion is a very tightly regulated process that, in vivo, very often requires specific chaperons to deliver and help incorporate the metal atom in the macromolecule. The lack of or inappropriate incorporation of metals along with genetic factors can lead to the mis-function of these proteins leading to disease. The mis-functions due to genetic alterations that lead to diseases like ALS (amyotrophic lateral sclerosis or motor neuron disease) and Creutzfeld Jacob disease (CJD) are now well recognised. Synchrotron radiation sources provide a unique set of structural tools, which in combination can prove extremely powerful in providing a comprehensive picture of these complex biological systems. In particular for metalloproteins, the combined use of X-ray crystallography, X-ray solution scattering and X-ray spectroscopy (XAFS) is extremely useful. We are currently engaged in a structural study where our aim is to characterize structurally and functionally metalloproteins and then transfer this knowledge to afford the problem of the mis-function of metalloproteins that lead to these terminal illnesses, either due to a gain of function/property or a loss of function/property. In this context, the benefits of adopting the `philosophy' being developed for the structural genomics effort are highlighted. [source]

    Introductory overview: X-ray absorption spectroscopy and structural genomics

    Isabella Ascone
    A special issue of the journal is presented, dedicated to biological applications of X-ray absorption spectroscopy (BioXAS) and examining the role of this technique in post-genomic biology. The issue confirms that BioXAS has come of age and it can be expected to make a significant contribution in the structural genomics effort on metalloproteins, which are estimated to make up about 30% of proteins coded by genomes. [source]

    Structure of the conserved hypothetical protein MAL13P1.257 from Plasmodium falciparum

    Margaret A. Holmes
    The structure of a conserved hypothetical protein, PlasmoDB sequence MAL13P1.257 from Plasmodium falciparum, Pfam sequence family PF05907, has been determined as part of the structural genomics effort of the Structural Genomics of Pathogenic Protozoa consortium. The structure was determined by multiple-wavelength anomalous dispersion at 2.17, resolution. The structure is almost entirely ,-sheet; it consists of 15 ,-strands and one short 310 -helix and represents a new protein fold. The packing of the two monomers in the asymmetric unit indicates that the biological unit may be a dimer. [source]

    Object-oriented approach to drug design enabled by NMR SOLVE: First real-time structural tool for characterizing protein,ligand interactions

    Daniel S. Sem
    Abstract As a result of genomics efforts, the number of protein drug targets is expected to increase by an order of magnitude. Functional genomics efforts are identifying these targets, while structural genomics efforts are determining structures for many of them. However, there is a significant gap in going from structural information for a protein target to a high affinity (Kd,<,100 nM) inhibitor, and the problem is multiplied by the sheer number of new targets now available. nature frequently designs proteins in classes that are related by the reuse, through gene duplication events, of cofactor binding domains. This reuse of functional domains is an efficient way to build related proteins in that it is object-oriented. There is a growing realization that the most efficient drug design strategies for attacking the mass of targets coming from genomics efforts will be systems-based approaches that attack groups of related proteins in parallel. We propose that the most effective drug design strategy will be one that parallels the object-oriented manner by which nature designed the gene families themselves. IOPE (Integrated Object-Oriented PharmacoEngineering) is such an approach. It is a three-step technology to build focused combinatorial libraries of potential inhibitors for major families and sub-families of enzymes, using cogent NMR data derived from representatives of these protein families. The NMR SOLVE (Structurally Oriented Library Valency Engineering) data used to design these libraries are gathered in days, and data can be obtained for large proteins (>,170 kDa). Furthermore, the process is fully object-oriented in that once a given bi-ligand is identified for a target, potency is retained if different cofactor mimics are swapped. This gives the drug design process maximum flexibility, allowing for the more facile transition from in vitro potency to in vivo efficacy. J. Cell. Biochem. Suppl. 37: 99,105, 2001. 2002 Wiley-Liss, Inc. [source]

    Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction

    Soheila Emamzadah
    Microfluidics is a promising technology for the rapid identification of protein crystallization conditions. However, most of the existing systems utilize silicone elastomers as the chip material which, despite its many benefits, is highly permeable to water vapour. This limits the time available for protein crystallization to less than a week. Here, the use of a cyclic olefin homopolymer-based microfluidics system for protein crystallization and in situ X-ray diffraction is described. Liquid handling in this system is performed in 2,mm thin transparent cards which contain 500 chambers, each with a volume of 320,nl. Microbatch, vapour-diffusion and free-interface diffusion protocols for protein crystallization were implemented and crystals were obtained of a number of proteins, including chicken lysozyme, bovine trypsin, a human p53 protein containing both the DNA-binding and oligomerization domains bound to DNA and a functionally important domain of Arabidopsis Morpheus' molecule 1 (MOM1). The latter two polypeptides have not been crystallized previously. For X-ray diffraction analysis, either the cards were opened to allow mounting of the crystals on loops or the crystals were exposed to X-rays in situ. For lysozyme, an entire X-ray diffraction data set at 1.5, resolution was collected without removing the crystal from the card. Thus, cyclic olefin homopolymer-based microfluidics systems have the potential to further automate protein crystallization and structural genomics efforts. [source]

    Case-controlled structure validation

    Randy J. Read
    Although many factors influence the quality of a macromolecular crystal structure, validation criteria are usually only calibrated using one of these factors, the resolution. For many purposes this is sufficient, but there are times when one wishes to compare one set of structures with another and the comparison may be invalidated by systematic differences between the sets in factors other than resolution. This problem can be circumvented by borrowing from medicine the idea of the case-matched control: each structure of interest is matched with a control structure that has similar values for all relevant factors considered in this study. In addition to resolution, these include the size of the structure (as measured by the volume of the asymmetric unit) and the year of deposition. This approach has been applied to address two questions: whether structures from structural genomics efforts reach the same level of quality as structures from traditional sources and whether the impact factor of the journal in which a structure is published correlates with structure quality. In both cases, once factors influencing quality have been controlled in the comparison, there is little evidence for a systematic difference in quality. [source]